Job ID = 6367486 SRX = SRX331243 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:27:06 prefetch.2.10.7: 1) Downloading 'SRR947475'... 2020-06-15T23:27:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:27:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:27:43 prefetch.2.10.7: 'SRR947475' is valid 2020-06-15T23:27:43 prefetch.2.10.7: 1) 'SRR947475' was downloaded successfully Read 6100097 spots for SRR947475/SRR947475.sra Written 6100097 spots for SRR947475/SRR947475.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:55 6100097 reads; of these: 6100097 (100.00%) were unpaired; of these: 147793 (2.42%) aligned 0 times 5168784 (84.73%) aligned exactly 1 time 783520 (12.84%) aligned >1 times 97.58% overall alignment rate Time searching: 00:00:55 Overall time: 00:00:55 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 642171 / 5952304 = 0.1079 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:30:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:30:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:37: 1000000 INFO @ Tue, 16 Jun 2020 08:30:42: 2000000 INFO @ Tue, 16 Jun 2020 08:30:47: 3000000 INFO @ Tue, 16 Jun 2020 08:30:53: 4000000 INFO @ Tue, 16 Jun 2020 08:30:58: 5000000 INFO @ Tue, 16 Jun 2020 08:30:59: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:30:59: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:30:59: #1 total tags in treatment: 5310133 INFO @ Tue, 16 Jun 2020 08:30:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:30:59: #1 tags after filtering in treatment: 5310133 INFO @ Tue, 16 Jun 2020 08:30:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:00: #2 number of paired peaks: 216 WARNING @ Tue, 16 Jun 2020 08:31:00: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:00: start model_add_line... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:31:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:00: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:31:00: #2 alternative fragment length(s) may be 31,66,119,170,229,542 bps INFO @ Tue, 16 Jun 2020 08:31:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.05_model.r WARNING @ Tue, 16 Jun 2020 08:31:00: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:00: #2 You may need to consider one of the other alternative d(s): 31,66,119,170,229,542 WARNING @ Tue, 16 Jun 2020 08:31:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:31:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:31:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:31:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:07: 1000000 INFO @ Tue, 16 Jun 2020 08:31:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:12: 2000000 INFO @ Tue, 16 Jun 2020 08:31:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.05_summits.bed INFO @ Tue, 16 Jun 2020 08:31:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (222 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:31:17: 3000000 INFO @ Tue, 16 Jun 2020 08:31:22: 4000000 INFO @ Tue, 16 Jun 2020 08:31:27: 5000000 INFO @ Tue, 16 Jun 2020 08:31:28: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:28: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:28: #1 total tags in treatment: 5310133 INFO @ Tue, 16 Jun 2020 08:31:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:31:28: #1 tags after filtering in treatment: 5310133 INFO @ Tue, 16 Jun 2020 08:31:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:29: #2 number of paired peaks: 216 WARNING @ Tue, 16 Jun 2020 08:31:29: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:29: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:31:29: #2 alternative fragment length(s) may be 31,66,119,170,229,542 bps INFO @ Tue, 16 Jun 2020 08:31:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.10_model.r WARNING @ Tue, 16 Jun 2020 08:31:29: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:29: #2 You may need to consider one of the other alternative d(s): 31,66,119,170,229,542 WARNING @ Tue, 16 Jun 2020 08:31:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:31:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:29: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:31:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:31:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:37: 1000000 INFO @ Tue, 16 Jun 2020 08:31:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:42: 2000000 INFO @ Tue, 16 Jun 2020 08:31:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.10_summits.bed INFO @ Tue, 16 Jun 2020 08:31:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (75 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:31:46: 3000000 INFO @ Tue, 16 Jun 2020 08:31:51: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:31:56: 5000000 INFO @ Tue, 16 Jun 2020 08:31:58: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:58: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:58: #1 total tags in treatment: 5310133 INFO @ Tue, 16 Jun 2020 08:31:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:31:58: #1 tags after filtering in treatment: 5310133 INFO @ Tue, 16 Jun 2020 08:31:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:58: #2 number of paired peaks: 216 WARNING @ Tue, 16 Jun 2020 08:31:58: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:58: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:31:58: #2 alternative fragment length(s) may be 31,66,119,170,229,542 bps INFO @ Tue, 16 Jun 2020 08:31:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.20_model.r WARNING @ Tue, 16 Jun 2020 08:31:58: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:58: #2 You may need to consider one of the other alternative d(s): 31,66,119,170,229,542 WARNING @ Tue, 16 Jun 2020 08:31:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:31:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:32:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331243/SRX331243.20_summits.bed INFO @ Tue, 16 Jun 2020 08:32:14: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis CompletedMACS2peakCalling